From 6d6ff73a2082f83ced2d5a74e1abd089ece41f6c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 6 Jan 2021 22:21:32 -0600
Subject: [PATCH] Fix log in infer species if ambiguous
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index cec1b29..9b458f4 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -810,11 +810,13 @@ process inferMetadata {
species="Homo sapiens"
bam="GRCh.sampled.sorted.bam"
bed="./GRCh/genome.bed"
+ echo -e "LOG: inference of species results in: \${species}" >> ${repRID}.inferMetadata.log
elif [ 1 -eq \$(echo \$(expr \${align_mo} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_hu} "<" 40)) ]
then
species="Mus musculus"
bam="GRCm.sampled.sorted.bam"
bed="./GRCm/genome.bed"
+ echo -e "LOG: inference of species results in: \${species}" >> ${repRID}.inferMetadata.log
else
echo -e "LOG: ERROR - inference of species returns an ambiguous result: hu=\${align_hu} mo=\${align_mo}" >> ${repRID}.inferMetadata.log
if [ "${speciesForce}" == "" ]
@@ -836,8 +838,6 @@ process inferMetadata {
bam="GRCm.sampled.sorted.bam"
bed="./GRCm/genome.bed"
fi
- else
- echo -e "LOG: inference of species results in: \${species}" >> ${repRID}.inferMetadata.log
fi
# infer experimental setting from dedup bam
--
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